-package jalview.analysis;\r
-\r
-import java.util.Hashtable;\r
-import java.util.Vector;\r
-\r
-import jalview.datamodel.AlignedCodonFrame;\r
-import jalview.datamodel.Alignment;\r
-import jalview.datamodel.AlignmentAnnotation;\r
-import jalview.datamodel.AlignmentI;\r
-import jalview.datamodel.Annotation;\r
-import jalview.datamodel.ColumnSelection;\r
-import jalview.datamodel.FeatureProperties;\r
-import jalview.datamodel.Mapping;\r
-import jalview.datamodel.Sequence;\r
-import jalview.datamodel.SequenceFeature;\r
-import jalview.datamodel.SequenceI;\r
-import jalview.schemes.ResidueProperties;\r
-import jalview.util.MapList;\r
-import jalview.util.ShiftList;\r
-\r
-public class Dna\r
-{\r
- /**\r
- * \r
- * @param cdp1\r
- * @param cdp2\r
- * @return -1 if cdp1 aligns before cdp2, 0 if in the same column or cdp2 is\r
- * null, +1 if after cdp2\r
- */\r
- private static int compare_codonpos(int[] cdp1, int[] cdp2)\r
- {\r
- if (cdp2 == null\r
- || (cdp1[0] == cdp2[0] && cdp1[1] == cdp2[1] && cdp1[2] == cdp2[2]))\r
- return 0;\r
- if (cdp1[0] < cdp2[0] || cdp1[1] < cdp2[1] || cdp1[2] < cdp2[2])\r
- return -1; // one base in cdp1 precedes the corresponding base in the\r
- // other codon\r
- return 1; // one base in cdp1 appears after the corresponding base in the\r
- // other codon.\r
- }\r
-\r
- /**\r
- * DNA->mapped protein sequence alignment translation given set of sequences\r
- * 1. id distinct coding regions within selected region for each sequence 2.\r
- * generate peptides based on inframe (or given) translation or (optionally\r
- * and where specified) out of frame translations (annotated appropriately) 3.\r
- * align peptides based on codon alignment\r
- */\r
- /**\r
- * id potential products from dna 1. search for distinct products within\r
- * selected region for each selected sequence 2. group by associated DB type.\r
- * 3. return as form for input into above function\r
- */\r
- /**\r
- * \r
- */\r
- /**\r
- * create a new alignment of protein sequences by an inframe translation of\r
- * the provided NA sequences\r
- * \r
- * @param selection\r
- * @param seqstring\r
- * @param viscontigs\r
- * @param gapCharacter\r
- * @param annotations\r
- * @param aWidth\r
- * @return\r
- */\r
- public static AlignmentI CdnaTranslate(SequenceI[] selection,\r
- String[] seqstring, int viscontigs[], char gapCharacter,\r
- AlignmentAnnotation[] annotations, int aWidth)\r
- {\r
- AlignedCodonFrame codons = new AlignedCodonFrame(aWidth); // stores hash of\r
- // subsequent\r
- // positions for\r
- // each codon\r
- // start position\r
- // in alignment\r
- int s, sSize = selection.length;\r
- Vector pepseqs = new Vector();\r
- for (s = 0; s < sSize; s++)\r
- {\r
- SequenceI newseq = translateCodingRegion(selection[s], seqstring[s],\r
- viscontigs, codons, gapCharacter);\r
- if (newseq != null)\r
- {\r
- pepseqs.addElement(newseq);\r
- }\r
- }\r
- if (codons.aaWidth == 0)\r
- return null;\r
- SequenceI[] newseqs = new SequenceI[pepseqs.size()];\r
- pepseqs.copyInto(newseqs);\r
- AlignmentI al = new Alignment(newseqs);\r
- al.padGaps(); // ensure we look aligned.\r
- al.setDataset(null);\r
- translateAlignedAnnotations(annotations, al, codons);\r
- al.addCodonFrame(codons);\r
- return al;\r
- }\r
-\r
- /**\r
- * translate na alignment annotations onto translated amino acid alignment al\r
- * using codon mapping codons\r
- * \r
- * @param annotations\r
- * @param al\r
- * @param codons\r
- */\r
- public static void translateAlignedAnnotations(\r
- AlignmentAnnotation[] annotations, AlignmentI al,\r
- AlignedCodonFrame codons)\r
- {\r
- // //////////////////////////////\r
- // Copy annotations across\r
- //\r
- // Can only do this for columns with consecutive codons, or where\r
- // annotation is sequence associated.\r
-\r
- int pos, a, aSize;\r
- if (annotations != null)\r
- {\r
- for (int i = 0; i < annotations.length; i++)\r
- {\r
- // Skip any autogenerated annotation\r
- if (annotations[i].autoCalculated)\r
- {\r
- continue;\r
- }\r
-\r
- aSize = codons.getaaWidth(); // aa alignment width.\r
- jalview.datamodel.Annotation[] anots = (annotations[i].annotations == null) ? null\r
- : new jalview.datamodel.Annotation[aSize];\r
- if (anots != null)\r
- {\r
- for (a = 0; a < aSize; a++)\r
- {\r
- // process through codon map.\r
- if (codons.codons[a] != null\r
- && codons.codons[a][0] == (codons.codons[a][2] - 2))\r
- {\r
- pos = codons.codons[a][0];\r
- if (annotations[i].annotations[pos] == null\r
- || annotations[i].annotations[pos] == null)\r
- continue;\r
- // We just take the annotation in the first base in the codon\r
- anots[a] = new Annotation(annotations[i].annotations[pos]);\r
- }\r
- }\r
- }\r
-\r
- jalview.datamodel.AlignmentAnnotation aa = new jalview.datamodel.AlignmentAnnotation(\r
- annotations[i].label, annotations[i].description, anots);\r
- if (annotations[i].hasScore)\r
- {\r
- aa.setScore(annotations[i].getScore());\r
- }\r
- if (annotations[i].sequenceRef != null)\r
- {\r
- SequenceI aaSeq = codons\r
- .getAaForDnaSeq(annotations[i].sequenceRef);\r
- if (aaSeq != null)\r
- {\r
- // aa.compactAnnotationArray(); // throw away alignment annotation\r
- // positioning\r
- aa.setSequenceRef(aaSeq);\r
- aa.createSequenceMapping(aaSeq, aaSeq.getStart(), true); // rebuild\r
- // mapping\r
- aa.adjustForAlignment();\r
- aaSeq.addAlignmentAnnotation(aa);\r
- }\r
-\r
- }\r
- al.addAnnotation(aa);\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * Translate a na sequence\r
- * \r
- * @param selection\r
- * @param seqstring\r
- * @param viscontigs\r
- * @param codons\r
- * @param gapCharacter\r
- * @param newSeq\r
- * @return sequence ready to be added to alignment.\r
- */\r
- public static SequenceI translateCodingRegion(SequenceI selection,\r
- String seqstring, int[] viscontigs, AlignedCodonFrame codons,\r
- char gapCharacter)\r
- {\r
- ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring\r
- // intervals\r
- int vc, scontigs[] = new int[viscontigs.length];\r
- int npos = 0;\r
- for (vc = 0; vc < viscontigs.length; vc += 2)\r
- {\r
- vismapping.addShift(npos, viscontigs[vc]);\r
- scontigs[vc] = npos;\r
- npos += viscontigs[vc + 1];\r
- scontigs[vc + 1] = npos;\r
- }\r
-\r
- StringBuffer protein = new StringBuffer();\r
- String seq = seqstring.replace('U', 'T');\r
- char codon[] = new char[3];\r
- int cdp[] = new int[3], rf = 0, lastnpos = 0, nend;\r
- int aspos = 0;\r
- int resSize = 0;\r
- for (npos = 0, nend = seq.length(); npos < nend; npos++)\r
- {\r
- if (!jalview.util.Comparison.isGap(seq.charAt(npos)))\r
- {\r
- cdp[rf] = npos; // store position\r
- codon[rf++] = seq.charAt(npos); // store base\r
- }\r
- // filled an RF yet ?\r
- if (rf == 3)\r
- {\r
- String aa = ResidueProperties.codonTranslate(new String(codon));\r
- rf = 0;\r
- if (aa == null)\r
- aa = String.valueOf(gapCharacter);\r
- else\r
- {\r
- if (aa.equals("STOP"))\r
- {\r
- aa = "X";\r
- }\r
- resSize++;\r
- }\r
- // insert/delete gaps prior to this codon - if necessary\r
- boolean findpos = true;\r
- while (findpos)\r
- {\r
- // first ensure that the codons array is long enough.\r
- codons.checkCodonFrameWidth(aspos);\r
- // now check to see if we place the aa at the current aspos in the\r
- // protein alignment\r
- switch (Dna.compare_codonpos(cdp, codons.codons[aspos]))\r
- {\r
- case -1:\r
- codons.insertAAGap(aspos, gapCharacter);\r
- findpos = false;\r
- break;\r
- case +1:\r
- // this aa appears after the aligned codons at aspos, so prefix it\r
- // with a gap\r
- aa = "" + gapCharacter + aa;\r
- aspos++;\r
- if (aspos >= codons.aaWidth)\r
- codons.aaWidth = aspos + 1;\r
- break; // check the next position for alignment\r
- case 0:\r
- // codon aligns at aspos position.\r
- findpos = false;\r
- }\r
- }\r
- // codon aligns with all other sequence residues found at aspos\r
- protein.append(aa);\r
- lastnpos = npos;\r
- if (codons.codons[aspos] == null)\r
- {\r
- // mark this column as aligning to this aligned reading frame\r
- codons.codons[aspos] = new int[]\r
- { cdp[0], cdp[1], cdp[2] };\r
- }\r
- aspos++;\r
- if (aspos >= codons.aaWidth)\r
- codons.aaWidth = aspos + 1;\r
- }\r
- }\r
- if (resSize > 0)\r
- {\r
- SequenceI newseq = new Sequence(selection.getName(), protein\r
- .toString());\r
- if (rf != 0)\r
- {\r
- jalview.bin.Cache.log\r
- .debug("trimming contigs for incomplete terminal codon.");\r
- // map and trim contigs to ORF region\r
- vc = scontigs.length - 1;\r
- lastnpos = vismapping.shift(lastnpos); // place npos in context of\r
- // whole dna alignment (rather\r
- // than visible contigs)\r
- // incomplete ORF could be broken over one or two visible contig\r
- // intervals.\r
- while (vc >= 0 && scontigs[vc] > lastnpos)\r
- {\r
- if (vc > 0 && scontigs[vc - 1] > lastnpos)\r
- {\r
- vc -= 2;\r
- }\r
- else\r
- {\r
- // correct last interval in list.\r
- scontigs[vc] = lastnpos;\r
- }\r
- }\r
-\r
- if (vc > 0 && (vc + 1) < scontigs.length)\r
- {\r
- // truncate map list to just vc elements\r
- int t[] = new int[vc + 1];\r
- System.arraycopy(scontigs, 0, t, 0, vc + 1);\r
- scontigs = t;\r
- }\r
- if (vc <= 0)\r
- scontigs = null;\r
- }\r
- if (scontigs != null)\r
- {\r
- npos = 0;\r
- // Find sequence position for scontigs positions on the nucleotide\r
- // sequence string we were passed.\r
- for (vc = 0; vc < viscontigs.length; vc += 2)\r
- {\r
- scontigs[vc] = selection.findPosition(scontigs[vc]); // not from 1!\r
- npos += viscontigs[vc];\r
- scontigs[vc + 1] = selection\r
- .findPosition(npos + scontigs[vc + 1]); // exclusive\r
- if (scontigs[vc + 1] == selection.getEnd())\r
- break;\r
- }\r
- // trim trailing empty intervals.\r
- if ((vc + 2) < scontigs.length)\r
- {\r
- int t[] = new int[vc + 2];\r
- System.arraycopy(scontigs, 0, t, 0, vc + 2);\r
- scontigs = t;\r
- }\r
-\r
- MapList map = new MapList(scontigs, new int[]\r
- { 1, resSize }, 3, 1); // TODO: store mapping on newSeq for linked\r
- // DNA/Protein viewing.\r
- transferCodedFeatures(selection, newseq, map, null, null);\r
- SequenceI rseq = newseq.deriveSequence(); // construct a dataset\r
- // sequence for our new\r
- // peptide, regardless.\r
- // store a mapping (this actually stores a mapping between the dataset\r
- // sequences for the two sequences\r
- codons.addMap(selection, newseq, map);\r
- return rseq;\r
- }\r
- }\r
- // register the mapping somehow\r
- // \r
- return null;\r
- }\r
-\r
- /**\r
- * Given a peptide newly translated from a dna sequence, copy over and set any\r
- * features on the peptide from the DNA. If featureTypes is null, all features\r
- * on the dna sequence are searched (rather than just the displayed ones), and\r
- * similarly for featureGroups.\r
- * \r
- * @param dna\r
- * @param pep\r
- * @param map\r
- * @param featureTypes\r
- * hash who's keys are the displayed feature type strings\r
- * @param featureGroups\r
- * hash where keys are feature groups and values are Boolean objects\r
- * indicating if they are displayed.\r
- */\r
- private static void transferCodedFeatures(SequenceI dna, SequenceI pep,\r
- MapList map, Hashtable featureTypes, Hashtable featureGroups)\r
- {\r
- SequenceFeature[] sf = dna.getDatasetSequence().getSequenceFeatures();\r
- Boolean fgstate;\r
- jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils\r
- .selectRefs(dna.getDBRef(),\r
- jalview.datamodel.DBRefSource.DNACODINGDBS);\r
- if (dnarefs != null)\r
- {\r
- // intersect with pep\r
- for (int d = 0; d < dnarefs.length; d++)\r
- {\r
- Mapping mp = dnarefs[d].getMap();\r
- if (mp != null)\r
- {\r
- }\r
- }\r
- }\r
- if (sf != null)\r
- {\r
- for (int f = 0; f < sf.length; f++)\r
- {\r
- fgstate = (featureGroups == null) ? null : ((Boolean) featureGroups\r
- .get(sf[f].featureGroup));\r
- if ((featureTypes == null || featureTypes.containsKey(sf[f]\r
- .getType()))\r
- && (fgstate == null || fgstate.booleanValue()))\r
- {\r
- if (FeatureProperties.isCodingFeature(null, sf[f].getType()))\r
- {\r
- // if (map.intersectsFrom(sf[f].begin, sf[f].end))\r
- {\r
-\r
- }\r
- }\r
- }\r
- }\r
- }\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.analysis;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AlignedCodon;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
+import jalview.util.ShiftList;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.Iterator;
+import java.util.List;
+
+public class Dna
+{
+ private static final String STOP_ASTERIX = "*";
+
+ private static final Comparator<AlignedCodon> comparator = new CodonComparator();
+
+ /*
+ * 'final' variables describe the inputs to the translation, which should not
+ * be modified.
+ */
+ private final List<SequenceI> selection;
+
+ private final String[] seqstring;
+
+ private final Iterator<int[]> contigs;
+
+ private final char gapChar;
+
+ private final AlignmentAnnotation[] annotations;
+
+ private final int dnaWidth;
+
+ private final AlignmentI dataset;
+
+ private ShiftList vismapping;
+
+ private int[] startcontigs;
+
+ /*
+ * Working variables for the translation.
+ *
+ * The width of the translation-in-progress protein alignment.
+ */
+ private int aaWidth = 0;
+
+ /*
+ * This array will be built up so that position i holds the codon positions
+ * e.g. [7, 9, 10] that match column i (base 0) in the aligned translation.
+ * Note this implies a contract that if two codons do not align exactly, their
+ * translated products must occupy different column positions.
+ */
+ private AlignedCodon[] alignedCodons;
+
+ /**
+ * Constructor given a viewport and the visible contigs.
+ *
+ * @param viewport
+ * @param visibleContigs
+ */
+ public Dna(AlignViewportI viewport, Iterator<int[]> visibleContigs)
+ {
+ this.selection = Arrays.asList(viewport.getSequenceSelection());
+ this.seqstring = viewport.getViewAsString(true);
+ this.contigs = visibleContigs;
+ this.gapChar = viewport.getGapCharacter();
+ this.annotations = viewport.getAlignment().getAlignmentAnnotation();
+ this.dnaWidth = viewport.getAlignment().getWidth();
+ this.dataset = viewport.getAlignment().getDataset();
+ initContigs();
+ }
+
+ /**
+ * Initialise contigs used as starting point for translateCodingRegion
+ */
+ private void initContigs()
+ {
+ vismapping = new ShiftList(); // map from viscontigs to seqstring
+ // intervals
+
+ int npos = 0;
+ int[] lastregion = null;
+ ArrayList<Integer> tempcontigs = new ArrayList<>();
+ while (contigs.hasNext())
+ {
+ int[] region = contigs.next();
+ if (lastregion == null)
+ {
+ vismapping.addShift(npos, region[0]);
+ }
+ else
+ {
+ // hidden region
+ vismapping.addShift(npos, region[0] - lastregion[1] + 1);
+ }
+ lastregion = region;
+ tempcontigs.add(region[0]);
+ tempcontigs.add(region[1]);
+ }
+
+ startcontigs = new int[tempcontigs.size()];
+ int i = 0;
+ for (Integer val : tempcontigs)
+ {
+ startcontigs[i] = val;
+ i++;
+ }
+ tempcontigs = null;
+ }
+
+ /**
+ * Test whether codon positions cdp1 should align before, with, or after cdp2.
+ * Returns zero if all positions match (or either argument is null). Returns
+ * -1 if any position in the first codon precedes the corresponding position
+ * in the second codon. Else returns +1 (some position in the second codon
+ * precedes the corresponding position in the first).
+ *
+ * Note this is not necessarily symmetric, for example:
+ * <ul>
+ * <li>compareCodonPos([2,5,6], [3,4,5]) returns -1</li>
+ * <li>compareCodonPos([3,4,5], [2,5,6]) also returns -1</li>
+ * </ul>
+ *
+ * @param ac1
+ * @param ac2
+ * @return
+ */
+ public static final int compareCodonPos(AlignedCodon ac1,
+ AlignedCodon ac2)
+ {
+ return comparator.compare(ac1, ac2);
+ // return jalview_2_8_2compare(ac1, ac2);
+ }
+
+ /**
+ * Codon comparison up to Jalview 2.8.2. This rule is sequence order dependent
+ * - see http://issues.jalview.org/browse/JAL-1635
+ *
+ * @param ac1
+ * @param ac2
+ * @return
+ */
+ private static int jalview_2_8_2compare(AlignedCodon ac1,
+ AlignedCodon ac2)
+ {
+ if (ac1 == null || ac2 == null || (ac1.equals(ac2)))
+ {
+ return 0;
+ }
+ if (ac1.pos1 < ac2.pos1 || ac1.pos2 < ac2.pos2 || ac1.pos3 < ac2.pos3)
+ {
+ // one base in cdp1 precedes the corresponding base in the other codon
+ return -1;
+ }
+ // one base in cdp1 appears after the corresponding base in the other codon.
+ return 1;
+ }
+
+ /**
+ * Translates cDNA using the specified code table
+ *
+ * @return
+ */
+ public AlignmentI translateCdna(GeneticCodeI codeTable)
+ {
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+
+ alignedCodons = new AlignedCodon[dnaWidth];
+
+ int s;
+ int sSize = selection.size();
+ List<SequenceI> pepseqs = new ArrayList<>();
+ for (s = 0; s < sSize; s++)
+ {
+ SequenceI newseq = translateCodingRegion(selection.get(s),
+ seqstring[s], acf, pepseqs, codeTable);
+
+ if (newseq != null)
+ {
+ pepseqs.add(newseq);
+ SequenceI ds = newseq;
+ if (dataset != null)
+ {
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+ dataset.addSequence(ds);
+ }
+ }
+ }
+
+ SequenceI[] newseqs = pepseqs.toArray(new SequenceI[pepseqs.size()]);
+ AlignmentI al = new Alignment(newseqs);
+ // ensure we look aligned.
+ al.padGaps();
+ // link the protein translation to the DNA dataset
+ al.setDataset(dataset);
+ translateAlignedAnnotations(al, acf);
+ al.addCodonFrame(acf);
+ return al;
+ }
+
+ /**
+ * fake the collection of DbRefs with associated exon mappings to identify if
+ * a translation would generate distinct product in the currently selected
+ * region.
+ *
+ * @param selection
+ * @param viscontigs
+ * @return
+ */
+ public static boolean canTranslate(SequenceI[] selection,
+ int viscontigs[])
+ {
+ for (int gd = 0; gd < selection.length; gd++)
+ {
+ SequenceI dna = selection[gd];
+ List<DBRefEntry> dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
+ jalview.datamodel.DBRefSource.DNACODINGDBS);
+ if (dnarefs != null)
+ {
+ // intersect with pep
+ List<DBRefEntry> mappedrefs = new ArrayList<>();
+ List<DBRefEntry> refs = dna.getDBRefs();
+ for (int d = 0, nd = refs.size(); d < nd; d++)
+ {
+ DBRefEntry ref = refs.get(d);
+ if (ref.getMap() != null && ref.getMap().getMap() != null
+ && ref.getMap().getMap().getFromRatio() == 3
+ && ref.getMap().getMap().getToRatio() == 1)
+ {
+ mappedrefs.add(ref); // add translated protein maps
+ }
+ }
+ dnarefs = mappedrefs;// .toArray(new DBRefEntry[mappedrefs.size()]);
+ for (int d = 0, nd = dnarefs.size(); d < nd; d++)
+ {
+ Mapping mp = dnarefs.get(d).getMap();
+ if (mp != null)
+ {
+ for (int vc = 0, nv = viscontigs.length; vc < nv; vc += 2)
+ {
+ int[] mpr = mp.locateMappedRange(viscontigs[vc],
+ viscontigs[vc + 1]);
+ if (mpr != null)
+ {
+ return true;
+ }
+ }
+ }
+ }
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Translate nucleotide alignment annotations onto translated amino acid
+ * alignment using codon mapping codons
+ *
+ * @param al
+ * the translated protein alignment
+ */
+ protected void translateAlignedAnnotations(AlignmentI al,
+ AlignedCodonFrame acf)
+ {
+ // Can only do this for columns with consecutive codons, or where
+ // annotation is sequence associated.
+
+ if (annotations != null)
+ {
+ for (AlignmentAnnotation annotation : annotations)
+ {
+ /*
+ * Skip hidden or autogenerated annotation. Also (for now), RNA
+ * secondary structure annotation. If we want to show this against
+ * protein we need a smarter way to 'translate' without generating
+ * invalid (unbalanced) structure annotation.
+ */
+ if (annotation.autoCalculated || !annotation.visible
+ || annotation.isRNA())
+ {
+ continue;
+ }
+
+ int aSize = aaWidth;
+ Annotation[] anots = (annotation.annotations == null) ? null
+ : new Annotation[aSize];
+ if (anots != null)
+ {
+ for (int a = 0; a < aSize; a++)
+ {
+ // process through codon map.
+ if (a < alignedCodons.length && alignedCodons[a] != null
+ && alignedCodons[a].pos1 == (alignedCodons[a].pos3 - 2))
+ {
+ anots[a] = getCodonAnnotation(alignedCodons[a],
+ annotation.annotations);
+ }
+ }
+ }
+
+ AlignmentAnnotation aa = new AlignmentAnnotation(annotation.label,
+ annotation.description, anots);
+ aa.graph = annotation.graph;
+ aa.graphGroup = annotation.graphGroup;
+ aa.graphHeight = annotation.graphHeight;
+ if (annotation.getThreshold() != null)
+ {
+ aa.setThreshold(new GraphLine(annotation.getThreshold()));
+ }
+ if (annotation.hasScore)
+ {
+ aa.setScore(annotation.getScore());
+ }
+
+ final SequenceI seqRef = annotation.sequenceRef;
+ if (seqRef != null)
+ {
+ SequenceI aaSeq = acf.getAaForDnaSeq(seqRef);
+ if (aaSeq != null)
+ {
+ // aa.compactAnnotationArray(); // throw away alignment annotation
+ // positioning
+ aa.setSequenceRef(aaSeq);
+ // rebuild mapping
+ aa.createSequenceMapping(aaSeq, aaSeq.getStart(), true);
+ aa.adjustForAlignment();
+ aaSeq.addAlignmentAnnotation(aa);
+ }
+ }
+ al.addAnnotation(aa);
+ }
+ }
+ }
+
+ private static Annotation getCodonAnnotation(AlignedCodon is,
+ Annotation[] annotations)
+ {
+ // Have a look at all the codon positions for annotation and put the first
+ // one found into the translated annotation pos.
+ int contrib = 0;
+ Annotation annot = null;
+ for (int p = 1; p <= 3; p++)
+ {
+ int dnaCol = is.getBaseColumn(p);
+ if (annotations[dnaCol] != null)
+ {
+ if (annot == null)
+ {
+ annot = new Annotation(annotations[dnaCol]);
+ contrib = 1;
+ }
+ else
+ {
+ // merge with last
+ Annotation cpy = new Annotation(annotations[dnaCol]);
+ if (annot.colour == null)
+ {
+ annot.colour = cpy.colour;
+ }
+ if (annot.description == null || annot.description.length() == 0)
+ {
+ annot.description = cpy.description;
+ }
+ if (annot.displayCharacter == null)
+ {
+ annot.displayCharacter = cpy.displayCharacter;
+ }
+ if (annot.secondaryStructure == 0)
+ {
+ annot.secondaryStructure = cpy.secondaryStructure;
+ }
+ annot.value += cpy.value;
+ contrib++;
+ }
+ }
+ }
+ if (contrib > 1)
+ {
+ annot.value /= contrib;
+ }
+ return annot;
+ }
+
+ /**
+ * Translate a na sequence
+ *
+ * @param selection
+ * sequence displayed under viscontigs visible columns
+ * @param seqstring
+ * ORF read in some global alignment reference frame
+ * @param acf
+ * Definition of global ORF alignment reference frame
+ * @param proteinSeqs
+ * @param codeTable
+ * @return sequence ready to be added to alignment.
+ */
+ protected SequenceI translateCodingRegion(SequenceI selection,
+ String seqstring, AlignedCodonFrame acf,
+ List<SequenceI> proteinSeqs, GeneticCodeI codeTable)
+ {
+ List<int[]> skip = new ArrayList<>();
+ int[] skipint = null;
+
+ int npos = 0;
+ int vc = 0;
+
+ int[] scontigs = new int[startcontigs.length];
+ System.arraycopy(startcontigs, 0, scontigs, 0, startcontigs.length);
+
+ // allocate a roughly sized buffer for the protein sequence
+ StringBuilder protein = new StringBuilder(seqstring.length() / 2);
+ String seq = seqstring.replace('U', 'T').replace('u', 'T');
+ char codon[] = new char[3];
+ int cdp[] = new int[3];
+ int rf = 0;
+ int lastnpos = 0;
+ int nend;
+ int aspos = 0;
+ int resSize = 0;
+ for (npos = 0, nend = seq.length(); npos < nend; npos++)
+ {
+ if (!Comparison.isGap(seq.charAt(npos)))
+ {
+ cdp[rf] = npos; // store position
+ codon[rf++] = seq.charAt(npos); // store base
+ }
+ if (rf == 3)
+ {
+ /*
+ * Filled up a reading frame...
+ */
+ AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1],
+ cdp[2]);
+ String aa = codeTable.translate(new String(codon));
+ rf = 0;
+ final String gapString = String.valueOf(gapChar);
+ if (aa == null)
+ {
+ aa = gapString;
+ if (skipint == null)
+ {
+ skipint = new int[] { alignedCodon.pos1,
+ alignedCodon.pos3 /*
+ * cdp[0],
+ * cdp[2]
+ */ };
+ }
+ skipint[1] = alignedCodon.pos3; // cdp[2];
+ }
+ else
+ {
+ if (skipint != null)
+ {
+ // edit scontigs
+ skipint[0] = vismapping.shift(skipint[0]);
+ skipint[1] = vismapping.shift(skipint[1]);
+ for (vc = 0; vc < scontigs.length;)
+ {
+ if (scontigs[vc + 1] < skipint[0])
+ {
+ // before skipint starts
+ vc += 2;
+ continue;
+ }
+ if (scontigs[vc] > skipint[1])
+ {
+ // finished editing so
+ break;
+ }
+ // Edit the contig list to include the skipped region which did
+ // not translate
+ int[] t;
+ // from : s1 e1 s2 e2 s3 e3
+ // to s: s1 e1 s2 k0 k1 e2 s3 e3
+ // list increases by one unless one boundary (s2==k0 or e2==k1)
+ // matches, and decreases by one if skipint intersects whole
+ // visible contig
+ if (scontigs[vc] <= skipint[0])
+ {
+ if (skipint[0] == scontigs[vc])
+ {
+ // skipint at start of contig
+ // shift the start of this contig
+ if (scontigs[vc + 1] > skipint[1])
+ {
+ scontigs[vc] = skipint[1];
+ vc += 2;
+ }
+ else
+ {
+ if (scontigs[vc + 1] == skipint[1])
+ {
+ // remove the contig
+ t = new int[scontigs.length - 2];
+ if (vc > 0)
+ {
+ System.arraycopy(scontigs, 0, t, 0, vc - 1);
+ }
+ if (vc + 2 < t.length)
+ {
+ System.arraycopy(scontigs, vc + 2, t, vc,
+ t.length - vc + 2);
+ }
+ scontigs = t;
+ }
+ else
+ {
+ // truncate contig to before the skipint region
+ scontigs[vc + 1] = skipint[0] - 1;
+ vc += 2;
+ }
+ }
+ }
+ else
+ {
+ // scontig starts before start of skipint
+ if (scontigs[vc + 1] < skipint[1])
+ {
+ // skipint truncates end of scontig
+ scontigs[vc + 1] = skipint[0] - 1;
+ vc += 2;
+ }
+ else
+ {
+ // divide region to new contigs
+ t = new int[scontigs.length + 2];
+ System.arraycopy(scontigs, 0, t, 0, vc + 1);
+ t[vc + 1] = skipint[0];
+ t[vc + 2] = skipint[1];
+ System.arraycopy(scontigs, vc + 1, t, vc + 3,
+ scontigs.length - (vc + 1));
+ scontigs = t;
+ vc += 4;
+ }
+ }
+ }
+ }
+ skip.add(skipint);
+ skipint = null;
+ }
+ if (aa.equals(ResidueProperties.STOP))
+ {
+ aa = STOP_ASTERIX;
+ }
+ resSize++;
+ }
+ boolean findpos = true;
+ while (findpos)
+ {
+ /*
+ * Compare this codon's base positions with those currently aligned to
+ * this column in the translation.
+ */
+ final int compareCodonPos = compareCodonPos(alignedCodon,
+ alignedCodons[aspos]);
+ switch (compareCodonPos)
+ {
+ case -1:
+
+ /*
+ * This codon should precede the mapped positions - need to insert a
+ * gap in all prior sequences.
+ */
+ insertAAGap(aspos, proteinSeqs);
+ findpos = false;
+ break;
+
+ case +1:
+
+ /*
+ * This codon belongs after the aligned codons at aspos. Prefix it
+ * with a gap and try the next position.
+ */
+ aa = gapString + aa;
+ aspos++;
+ break;
+
+ case 0:
+
+ /*
+ * Exact match - codon 'belongs' at this translated position.
+ */
+ findpos = false;
+ }
+ }
+ protein.append(aa);
+ lastnpos = npos;
+ if (alignedCodons[aspos] == null)
+ {
+ // mark this column as aligning to this aligned reading frame
+ alignedCodons[aspos] = alignedCodon;
+ }
+ else if (!alignedCodons[aspos].equals(alignedCodon))
+ {
+ throw new IllegalStateException(
+ "Tried to coalign " + alignedCodons[aspos].toString()
+ + " with " + alignedCodon.toString());
+ }
+ if (aspos >= aaWidth)
+ {
+ // update maximum alignment width
+ aaWidth = aspos;
+ }
+ // ready for next translated reading frame alignment position (if any)
+ aspos++;
+ }
+ }
+ if (resSize > 0)
+ {
+ SequenceI newseq = new Sequence(selection.getName(),
+ protein.toString());
+ if (rf != 0)
+ {
+ final String errMsg = "trimming contigs for incomplete terminal codon.";
+ System.err.println(errMsg);
+ // map and trim contigs to ORF region
+ vc = scontigs.length - 1;
+ lastnpos = vismapping.shift(lastnpos); // place npos in context of
+ // whole dna alignment (rather
+ // than visible contigs)
+ // incomplete ORF could be broken over one or two visible contig
+ // intervals.
+ while (vc >= 0 && scontigs[vc] > lastnpos)
+ {
+ if (vc > 0 && scontigs[vc - 1] > lastnpos)
+ {
+ vc -= 2;
+ }
+ else
+ {
+ // correct last interval in list.
+ scontigs[vc] = lastnpos;
+ }
+ }
+
+ if (vc > 0 && (vc + 1) < scontigs.length)
+ {
+ // truncate map list to just vc elements
+ int t[] = new int[vc + 1];
+ System.arraycopy(scontigs, 0, t, 0, vc + 1);
+ scontigs = t;
+ }
+ if (vc <= 0)
+ {
+ scontigs = null;
+ }
+ }
+ if (scontigs != null)
+ {
+ npos = 0;
+ // map scontigs to actual sequence positions on selection
+ for (vc = 0; vc < scontigs.length; vc += 2)
+ {
+ scontigs[vc] = selection.findPosition(scontigs[vc]); // not from 1!
+ scontigs[vc + 1] = selection.findPosition(scontigs[vc + 1]); // exclusive
+ if (scontigs[vc + 1] == selection.getEnd())
+ {
+ break;
+ }
+ }
+ // trim trailing empty intervals.
+ if ((vc + 2) < scontigs.length)
+ {
+ int t[] = new int[vc + 2];
+ System.arraycopy(scontigs, 0, t, 0, vc + 2);
+ scontigs = t;
+ }
+ /*
+ * delete intervals in scontigs which are not translated. 1. map skip
+ * into sequence position intervals 2. truncate existing ranges and add
+ * new ranges to exclude untranslated regions. if (skip.size()>0) {
+ * Vector narange = new Vector(); for (vc=0; vc<scontigs.length; vc++) {
+ * narange.addElement(new int[] {scontigs[vc]}); } int sint=0,iv[]; vc =
+ * 0; while (sint<skip.size()) { skipint = (int[]) skip.elementAt(sint);
+ * do { iv = (int[]) narange.elementAt(vc); if (iv[0]>=skipint[0] &&
+ * iv[0]<=skipint[1]) { if (iv[0]==skipint[0]) { // delete beginning of
+ * range } else { // truncate range and create new one if necessary iv =
+ * (int[]) narange.elementAt(vc+1); if (iv[0]<=skipint[1]) { // truncate
+ * range iv[0] = skipint[1]; } else { } } } else if (iv[0]<skipint[0]) {
+ * iv = (int[]) narange.elementAt(vc+1); } } while (iv[0]) } }
+ */
+ MapList map = new MapList(scontigs, new int[] { 1, resSize }, 3, 1);
+
+ transferCodedFeatures(selection, newseq, map);
+
+ /*
+ * Construct a dataset sequence for our new peptide.
+ */
+ SequenceI rseq = newseq.deriveSequence();
+
+ /*
+ * Store a mapping (between the dataset sequences for the two
+ * sequences).
+ */
+ // SIDE-EFFECT: acf stores the aligned sequence reseq; to remove!
+ acf.addMap(selection, rseq, map);
+ return rseq;
+ }
+ }
+ // register the mapping somehow
+ //
+ return null;
+ }
+
+ /**
+ * Insert a gap into the aligned proteins and the codon mapping array.
+ *
+ * @param pos
+ * @param proteinSeqs
+ * @return
+ */
+ protected void insertAAGap(int pos, List<SequenceI> proteinSeqs)
+ {
+ aaWidth++;
+ for (SequenceI seq : proteinSeqs)
+ {
+ seq.insertCharAt(pos, gapChar);
+ }
+
+ checkCodonFrameWidth();
+ if (pos < aaWidth)
+ {
+ aaWidth++;
+
+ /*
+ * Shift from [pos] to the end one to the right, and null out [pos]
+ */
+ System.arraycopy(alignedCodons, pos, alignedCodons, pos + 1,
+ alignedCodons.length - pos - 1);
+ alignedCodons[pos] = null;
+ }
+ }
+
+ /**
+ * Check the codons array can accommodate a single insertion, if not resize
+ * it.
+ */
+ protected void checkCodonFrameWidth()
+ {
+ if (alignedCodons[alignedCodons.length - 1] != null)
+ {
+ /*
+ * arraycopy insertion would bump a filled slot off the end, so expand.
+ */
+ AlignedCodon[] c = new AlignedCodon[alignedCodons.length + 10];
+ System.arraycopy(alignedCodons, 0, c, 0, alignedCodons.length);
+ alignedCodons = c;
+ }
+ }
+
+ /**
+ * Given a peptide newly translated from a dna sequence, copy over and set any
+ * features on the peptide from the DNA.
+ *
+ * @param dna
+ * @param pep
+ * @param map
+ */
+ private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
+ MapList map)
+ {
+ // BH 2019.01.25 nop?
+ // List<DBRefEntry> dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
+ // DBRefSource.DNACODINGDBS);
+ // if (dnarefs != null)
+ // {
+ // // intersect with pep
+ // for (int d = 0, nd = dnarefs.size(); d < nd; d++)
+ // {
+ // Mapping mp = dnarefs.get(d).getMap();
+ // if (mp != null)
+ // {
+ // }
+ // }
+ // }
+ for (SequenceFeature sf : dna.getFeatures().getAllFeatures())
+ {
+ if (FeatureProperties.isCodingFeature(null, sf.getType()))
+ {
+ // if (map.intersectsFrom(sf[f].begin, sf[f].end))
+ {
+
+ }
+ }
+ }
+ }
+
+ /**
+ * Returns an alignment consisting of the reversed (and optionally
+ * complemented) sequences set in this object's constructor
+ *
+ * @param complement
+ * @return
+ */
+ public AlignmentI reverseCdna(boolean complement)
+ {
+ int sSize = selection.size();
+ List<SequenceI> reversed = new ArrayList<>();
+ for (int s = 0; s < sSize; s++)
+ {
+ SequenceI newseq = reverseSequence(selection.get(s).getName(),
+ seqstring[s], complement);
+
+ if (newseq != null)
+ {
+ reversed.add(newseq);
+ }
+ }
+
+ SequenceI[] newseqs = reversed.toArray(new SequenceI[reversed.size()]);
+ AlignmentI al = new Alignment(newseqs);
+ ((Alignment) al).createDatasetAlignment();
+ return al;
+ }
+
+ /**
+ * Returns a reversed, and optionally complemented, sequence. The new
+ * sequence's name is the original name with "|rev" or "|revcomp" appended.
+ * aAcCgGtT and DNA ambiguity codes are complemented, any other characters are
+ * left unchanged.
+ *
+ * @param seq
+ * @param complement
+ * @return
+ */
+ public static SequenceI reverseSequence(String seqName, String sequence,
+ boolean complement)
+ {
+ String newName = seqName + "|rev" + (complement ? "comp" : "");
+ char[] originalSequence = sequence.toCharArray();
+ int length = originalSequence.length;
+ char[] reversedSequence = new char[length];
+ int bases = 0;
+ for (int i = 0; i < length; i++)
+ {
+ char c = complement ? getComplement(originalSequence[i])
+ : originalSequence[i];
+ reversedSequence[length - i - 1] = c;
+ if (!Comparison.isGap(c))
+ {
+ bases++;
+ }
+ }
+ SequenceI reversed = new Sequence(newName, reversedSequence, 1, bases);
+ return reversed;
+ }
+
+ /**
+ * Answers the reverse complement of the input string
+ *
+ * @see #getComplement(char)
+ * @param s
+ * @return
+ */
+ public static String reverseComplement(String s)
+ {
+ StringBuilder sb = new StringBuilder(s.length());
+ for (int i = s.length() - 1; i >= 0; i--)
+ {
+ sb.append(Dna.getComplement(s.charAt(i)));
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Returns dna complement (preserving case) for aAcCgGtTuU. Ambiguity codes
+ * are treated as on http://reverse-complement.com/. Anything else is left
+ * unchanged.
+ *
+ * @param c
+ * @return
+ */
+ public static char getComplement(char c)
+ {
+ char result = c;
+ switch (c)
+ {
+ case '-':
+ case '.':
+ case ' ':
+ break;
+ case 'a':
+ result = 't';
+ break;
+ case 'A':
+ result = 'T';
+ break;
+ case 'c':
+ result = 'g';
+ break;
+ case 'C':
+ result = 'G';
+ break;
+ case 'g':
+ result = 'c';
+ break;
+ case 'G':
+ result = 'C';
+ break;
+ case 't':
+ result = 'a';
+ break;
+ case 'T':
+ result = 'A';
+ break;
+ case 'u':
+ result = 'a';
+ break;
+ case 'U':
+ result = 'A';
+ break;
+ case 'r':
+ result = 'y';
+ break;
+ case 'R':
+ result = 'Y';
+ break;
+ case 'y':
+ result = 'r';
+ break;
+ case 'Y':
+ result = 'R';
+ break;
+ case 'k':
+ result = 'm';
+ break;
+ case 'K':
+ result = 'M';
+ break;
+ case 'm':
+ result = 'k';
+ break;
+ case 'M':
+ result = 'K';
+ break;
+ case 'b':
+ result = 'v';
+ break;
+ case 'B':
+ result = 'V';
+ break;
+ case 'v':
+ result = 'b';
+ break;
+ case 'V':
+ result = 'B';
+ break;
+ case 'd':
+ result = 'h';
+ break;
+ case 'D':
+ result = 'H';
+ break;
+ case 'h':
+ result = 'd';
+ break;
+ case 'H':
+ result = 'D';
+ break;
+ }
+
+ return result;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff